RESUMEN
The genetic modules that contribute to human evolution are poorly understood. Here we investigate positive selection in the Epidermal Differentiation Complex locus for skin barrier adaptation in diverse HapMap human populations (CEU, JPT/CHB, and YRI). Using Composite of Multiple Signals and iSAFE, we identify selective sweeps for LCE1A-SMCP and involucrin (IVL) haplotypes associated with human migration out-of-Africa, reaching near fixation in European populations. CEU-IVL is associated with increased IVL expression and a known epidermis-specific enhancer. CRISPR/Cas9 deletion of the orthologous mouse enhancer in vivo reveals a functional requirement for the enhancer to regulate Ivl expression in cis. Reporter assays confirm increased regulatory and additive enhancer effects of CEU-specific polymorphisms identified at predicted IRF1 and NFIC binding sites in the IVL enhancer (rs4845327) and its promoter (rs1854779). Together, our results identify a selective sweep for a cis regulatory module for CEU-IVL, highlighting human skin barrier evolution for increased IVL expression out-of-Africa.
Asunto(s)
Elementos de Facilitación Genéticos , Regulación de la Expresión Génica/genética , Precursores de Proteínas/genética , Piel/metabolismo , África , Alelos , Animales , Sistemas CRISPR-Cas , Cromatina/genética , Cromatina/metabolismo , Secuenciación de Inmunoprecipitación de Cromatina , Bases de Datos Genéticas , Frecuencia de los Genes , Haplotipos , Humanos , Ratones , Ratones Endogámicos BALB C , Ratones Endogámicos C57BL , Polimorfismo Genético , Polimorfismo de Nucleótido Simple , Precursores de Proteínas/metabolismo , Sitios de Carácter Cuantitativo , RNA-Seq , Secuencias Reguladoras de Ácidos NucleicosAsunto(s)
Negro o Afroamericano/genética , Variaciones en el Número de Copia de ADN , Dermatitis Atópica/genética , Proteínas S100/genética , Adolescente , Adulto , Estudios de Casos y Controles , Niño , Dermatitis Atópica/epidemiología , Femenino , Proteínas Filagrina , Predisposición Genética a la Enfermedad , Humanos , Masculino , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple , Factores de Riesgo , Adulto JovenRESUMEN
Filaggrin (FLG) loss-of-function (LOF) variants are a major risk factor for the common inflammatory skin disease, atopic dermatitis (AD) and are often population-specific. African-American (AA) children are disproportionately affected with AD, often later developing asthma and/or allergic rhinitis and comprise an atopy health disparity group for which the role of FLG LOF is not well known. Discovery of FLG LOF using exome sequencing is challenging given the known difficulties for accurate short-read alignment to FLG's high homology repeat variation. Here, we employed an array-based sequencing approach to tile across each FLG repeat and discover FLG LOF in a well-characterized cohort of AA children with moderate-to-severe AD. Five FLG LOF were identified in 23% of our cohort. Two novel FLG LOF singletons, c.488delG and p.S3101*, were discovered as well as p.R501*, p.R826* and p.S3316* previously reported for AD. p.S3316* (rs149484917) is likely an African ancestral FLG LOF, reported in African individuals in ExAC (Exome Aggregation Consortium), Exome Variant Server (ESP), and 4 African 1000G population databases (ESN, MSL, ASW, and ACB). The proportion of FLG LOF (11.5%) among the total FLG alleles in our cohort was significantly higher in comparisons with FLG LOF reported for African individuals in ExAC (2.5%; P = 4.3 × 10-4 ) and ESP (1.7%; P = 3.5 × 10-5 ) suggesting a disease-enrichment effect for FLG LOF. Our results demonstrate the utility of array-based sequencing in discovering FLG LOF, including novel and population-specific, which are of higher prevalence in our AA severe AD group than previously reported.
Asunto(s)
Negro o Afroamericano/genética , Dermatitis Atópica/genética , Proteínas de Filamentos Intermediarios/genética , Mutación con Pérdida de Función , Análisis de Secuencia de ADN/métodos , Adolescente , Alelos , Niño , Preescolar , Exoma , Proteínas Filagrina , Humanos , Lactante , Análisis de Secuencia por Matrices de Oligonucleótidos , Índice de Severidad de la EnfermedadAsunto(s)
Negro o Afroamericano , Dermatitis Atópica/genética , Proteínas de Filamentos Intermediarios/genética , Mutación/genética , Adolescente , Asma/epidemiología , Niño , Preescolar , Comorbilidad , Dermatitis Atópica/etnología , Femenino , Proteínas Filagrina , Hipersensibilidad a los Alimentos/epidemiología , Genotipo , Humanos , Masculino , Secuencias Repetitivas de Ácidos Nucleicos/genética , Rinitis Alérgica/epidemiología , Rinitis Alérgica Estacional/epidemiología , PielRESUMEN
The epidermal differentiation complex (EDC) locus comprises a syntenic and linear cluster of genes whose concomitant expression is a hallmark feature of differentiation in the developing skin epidermis. Many of the EDC proteins are cross-linked together to form the cornified envelope, an essential and discrete unit of the mammalian skin barrier. The mechanism underlying coordinate transcriptional activation of the EDC is unknown. Within the human EDC, we identified an epidermal-specific regulatory enhancer, 923, which responded to the developmental and spatiotemporal cues at the onset of epidermal differentiation in the mouse embryo. Comparative chromosomal conformation capture assays in proliferating and differentiated primary mouse keratinocytes revealed multiple physiologically sensitive chromatin interactions between the 923 enhancer and EDC gene promoters, thus depicting the dynamic chromatin topology of the EDC. We elucidate a mechanistic link between c-Jun/AP-1 and 923, whereby AP-1- and 923-mediated EDC chromatin remodeling are required for functional EDC gene activation. Thus, we identify a critical enhancer/transcription factor axis governing the dynamic regulation of the EDC chromatin architecture and gene expression and provide a framework for future studies toward understanding gene regulation in cutaneous diseases.